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This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest.
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README.md


Quantify and annotate short reads in R


Overview

QuasR aims to cover the whole analysis workflow of typical ultra-high throughput sequencing experiments, starting from the raw sequence reads, over pre-processing and alignment, up to quantification. A single R script can contain all steps of a complete analysis, making it simple to document, reproduce or share the workflow containing all relevant details.

The QuasR package integrates the functionality of several R packages (such as IRanges and Rsamtools) and external software (e.g. bowtie, through the Rbowtie package).

The package was originally created for in house use at the Friedrich Miescher Institute. Current contributors include:

Functionality

The current QuasR release supports the analysis of single read and paired-end ChIP-seq (chromatin immuno-precipitation combined with sequencing), RNA-seq (gene expression profiling by sequencing of RNA) and Bis-seq (measurement of DNA methylation by sequencing of bisulfite-converted genomic DNA) experiments. Allele specific alignment and quantification is also supported in all of these experiment types. QuasR has been successfully used with data from Illumina, 454 Life Technologies and SOLiD sequencers, the latter by using bam files created externally QuasR.

Reference

QuasR has been described in:

"QuasR: Quantify and Annotate Short Reads in R"
Gaidatzis, D. and Lerch, A. and Hahne, F. and Stadler, M.B.
Bioinformatics 2015, 31(7):1130-1132.
PubMed: 25417205, doi: 10.1093/bioinformatics/btu781

Download from Bioconductor

QuasR download page

Software status

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Travis CI Linux Travis CI build status Codecov.io coverage status
Appveyor CI Windows AppVeyor build status NA
Bioc (devel) Multiple Bioconductor-devel Build Status NA
Bioc (release) Multiple Bioconductor-release Build Status NA
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